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Welcome to the TotalVibeSegmentator wiki!

Running an Example

You have to install Python and packages as described in the ReadMe.md and activate your environment.

conda activate TotalVibeSegmentator
#cd to the folder where you downloaded the GitHub files (the folder where the run_TotalVibeSegmentator.py is located)

Let's run some examples that were never seen during training. You can download all four examples from here

(Source: link Number s0284, s0286, s0287, s0288)

Unzip the file. For this example, we copied all files to a folder called 'example' where the run_TotalVibeSegmentator.py is located.

python run_TotalVibeSegmentator.py --img example/mri1.nii.gz --out_path  example/seg1.nii.gz

python run_TotalVibeSegmentator.py --img example/mri2.nii.gz --out_path  example/seg2.nii.gz

python run_TotalVibeSegmentator.py --img example/mri3.nii.gz --out_path  example/seg3.nii.gz

python run_TotalVibeSegmentator.py --img example/mri4.nii.gz --out_path  example/seg4.nii.gz

The segmentation is stored in "example/segX.nii.gz." You can view the results with ITKSnap by first drag-and-drop the mriX.nii.gz and then drag-and-drop the segX.nii.gz (with X is a number from before) and click on "Open as Segmentation"

To run this script on your data update the paths.